ClinVar Miner

Submissions for variant NM_032383.5(HPS3):c.1682_1683del (p.Cys561fs)

dbSNP: rs778152054
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000820215 SCV000960916 pathogenic not provided 2023-11-20 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Cys561Leufs*5) in the HPS3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in HPS3 are known to be pathogenic (PMID: 11590544). This variant is present in population databases (rs778152054, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with HPS3-related conditions. ClinVar contains an entry for this variant (Variation ID: 662551). For these reasons, this variant has been classified as Pathogenic.
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill RCV001095689 SCV001251492 likely pathogenic Hermansky-Pudlak syndrome 3 criteria provided, single submitter research HPS3 c.1682_1683delGT (p.C561fs) is a frameshift deletion of two nucleotides that is predicted to result in an nonfunctional HPS3 protein. This variant has not been described previously in the literature.
GeneDx RCV000820215 SCV002513228 pathogenic not provided 2022-05-04 criteria provided, single submitter clinical testing Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge
Baylor Genetics RCV001095689 SCV004200002 likely pathogenic Hermansky-Pudlak syndrome 3 2023-09-11 criteria provided, single submitter clinical testing

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